def test_custom_initialization() -> None:
assert Vec3Int.zeros() == Vec3Int(0, 0, 0)
assert Vec3Int.ones() == Vec3Int(1, 1, 1)
assert Vec3Int.full(4) == Vec3Int(4, 4, 4)
assert Vec3Int.ones() - Vec3Int.ones() == Vec3Int.zeros()
assert Vec3Int.full(4) == Vec3Int.ones() * 4
def merge_with_fallback_layer(
output_path: Path,
volume_annotation_path: Path,
segmentation_layer_path: Path,
) -> MagView:
assert not output_path.exists(), f"Dataset at {output_path} already exists"
# Prepare output dataset by creatign a shallow copy of the dataset
# determined by segmentation_layer_path, but do a deep copy of
# segmentation_layer_path itself (so that we can mutate it).
input_segmentation_dataset = wk.Dataset.open(
segmentation_layer_path.parent)
time_start("Prepare output dataset")
output_dataset = input_segmentation_dataset.shallow_copy_dataset(
output_path,
name=output_path.name,
make_relative=True,
layers_to_ignore=[segmentation_layer_path.name],
)
output_layer = output_dataset.add_copy_layer(segmentation_layer_path,
segmentation_layer_path.name)
time_stop("Prepare output dataset")
input_segmentation_mag = input_segmentation_dataset.get_layer(
segmentation_layer_path.name).get_finest_mag()
with temporary_annotation_view(
volume_annotation_path) as input_annotation_layer:
input_annotation_mag = input_annotation_layer.get_finest_mag()
bboxes = [
bbox.in_mag(input_annotation_mag._mag)
for bbox in input_annotation_mag.get_bounding_boxes_on_disk()
]
output_mag = output_layer.get_mag(input_segmentation_mag.mag)
cube_size = output_mag.info.chunk_size[
0] * output_mag.info.chunks_per_shard[0]
chunks_with_bboxes = BoundingBox.group_boxes_with_aligned_mag(
bboxes, Mag(cube_size))
assert (input_annotation_mag.info.chunks_per_shard == Vec3Int.ones()
), "volume annotation must have file_len=1"
assert (input_annotation_mag.info.voxel_type ==
input_segmentation_mag.info.voxel_type
), "Volume annotation must have same dtype as fallback layer"
chunk_count = 0
for chunk, bboxes in chunks_with_bboxes.items():
chunk_count += 1
logger.info(f"Processing chunk {chunk_count}...")
time_start("Read chunk")
data_buffer = output_mag.read(chunk.topleft,
chunk.size)[0, :, :, :]
time_stop("Read chunk")
time_start("Read/merge bboxes")
for bbox in bboxes:
read_data = input_annotation_mag.read(bbox.topleft, bbox.size)
data_buffer[bbox.offset(
-chunk.topleft).to_slices()] = read_data
time_stop("Read/merge bboxes")
time_start("Write chunk")
output_mag.write(data_buffer, chunk.topleft)
time_stop("Write chunk")
return output_mag